U-99 was one of the most successful German U-boats in the war, sinking 38 ships for a total tonnage of 244,658 GRT of Allied shipping in eight patrols. She damaged five more ships and took one vessel as a prize.

On 18 June, U-99 departed Kiel for operations in the North Sea west of Norway.[2] She was attacked by an Arado Ar-196 seaplane from the German battleship Scharnhorst, having been mistaken for a British submarine. Two days later, U-99 was attacked by two aircraft; minor damage was inflicted.[3] She returned to Kiel on 25 June.[2]

U-99 departed Wilhelmshaven on 27 June to patrol southwest of Ireland.[2] On 29 June, she was attacked by British aircraft. A crash dive was carried out with the result that the boat hit the seabed, causing some damage which was able to be repaired.[3] During this patrol, U-99 sank six ships.[2] A seventh was captured.[4] An attack on the 5,360 GRT Manistee was called off on 7 July, when the armed merchant ship fired upon the U-boat.[5] On 8 July, over 100 depth charges were dropped by the escorts of Convoy HX 53, but U-99 escaped undamaged.[3] The patrol ended on 21 July.[2]

On 25 July, U-99 departed Lorient for the North Atlantic. Four ships were sunk and three others damaged.[2] On the 31st, the escorts of Convoy OB 191 dropped 20 depth charges on the boat without effect. Later that evening, a flying boat also attacked her, again without causing any damage.[3] The patrol ended on 5 August.[2]

U-99 departed Lorient on 22 February 1941 to patrol in the North Atlantic; eight ships were sunk. U-99 was attacked herself, with severe damage inflicted. Kretschmer surrendered and scuttled the submarine with the loss of three lives.[2]

On 17 March 1941, U-99 had just fired the last of her torpedoes and sunk Korshamn when the Watch Officer spotted a destroyer, south-east of Iceland in approximate position 61°N12°W﻿ / ﻿61°N 12°W﻿ / 61; -12Coordinates: 61°N12°W﻿ / ﻿61°N 12°W﻿ / 61; -12. He immediately ordered a dive, contrary to Kretschmer's standing orders,[6] but once the boat was under it was quickly fixed on ASDIC and attacked by HMS Walker and Vanoc. U-99 was driven deep by the attack but was nonetheless severely damaged. Kretschmer had no choice but to surface; immediately a barrage of fire greeted the boat. Kretschmer sent a message to Donald Macintyre, Walker‍ '​s captain, "CAPTAIN TO CAPTAIN. I AM SUNKING [sic] PLEASE RESCUE MY CREW."[7] He then ordered that the boat should be scuttled. 40 crew, including Kretschmer, were rescued to become POWs, while three crewmen lost their lives. Macintyre took Kretschmer's binoculars as a souvenir.[8]